Introduction Evidence from sub-Saharan Africa, including Kenya, shows that negative beliefs about contraceptive methods are associated with non-use. However, little is known about the relationship between contraceptive beliefs and subsequent method choice. Methodology We used data from a two-year longitudinal survey of married women aged 15–39 years at enrollment from one urban site (Nairobi) and one rural site (Homa Bay) in Kenya. Analysis entails descriptive statistics and estimation of a conditional logit analysis to examine associations between method-specific beliefs and choice of injectables, implants or pills among women who were not using any method or were pregnant at baseline (round 1) but adopted these methods at 12-month follow-up (Nairobi, n = 221; Homa Bay n = 197). Results Beliefs about pills, injectables and implants among non-users were generally negative. With the partial exception of the pill in Nairobi, the majority thought that each method was likely to cause serious health problems, unpleasant side effects, menstrual disruption, and would be unsafe for long-term use. In both sites, satisfied past use of a method and the perception that a method is easy to use had a major influence on method choice. Concerns about menstrual disruption and safety for long-term use were unimportant in both sites. There were some marked differences between the two sites. Beliefs about long-term fertility impairment and perceived husband approval had strong influences on choice of injectables, implants or pills in the urban site but not in the rural site. Conclusion The relative importance of beliefs, some erroneous, in predisposing women to choose one method over another appears to be conditioned by the social context. There is need for family planning counseling programmes to pay attention to erroneous beliefs and misconceptions about contraceptives.